Dec 23, 2024

Public workspaceUnbiased MD simulations of POPI entry into VPS34KD

DOI
https://dx.doi.org/10.17504/protocols.io.dm6gp9y68vzp/v1
  • Ainara Claveras Cabezudo1,2,3,
  • Annan Cook4,3
  • 1Max Planck Institute of Biophysics;
  • 2IMPRS on Cellular Biophysics;
  • 3Aligning Science Across Parkinson's CRN;
  • 4University of California, Berkeley
Ainara Claveras Cabezudo
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DOI: https://dx.doi.org/10.17504/protocols.io.dm6gp9y68vzp/v1
Protocol Citation: Ainara Claveras Cabezudo, Annan Cook 2024. Unbiased MD simulations of POPI entry into VPS34KD. protocols.io https://dx.doi.org/10.17504/protocols.io.dm6gp9y68vzp/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: December 22, 2024
Last Modified: December 23, 2024
Protocol Integer ID: 116785
Keywords: ASAPCRN, molecular dynamics simulations of the kinase domain, unbiased md simulations of popi entry, popi lipid, molecular dynamics simulation, analysis of popi entry, kinase domain, popi entry, vps34kd this protocol, vps34, vps34kd, membrane, catalytic site
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: ASAP-000350
Abstract
This protocol details molecular dynamics simulations of the kinase domain of VPS34 in a membrane containing 15% of POPI lipids and analysis of POPI entry into the catalytic site.
Troubleshooting
Model Preparation
Use a conformation obtained of the full PI3KC3-C1 active complex engaged with the membrane as starting structure.
Isolate the C-terminal region of the VPS34KD catalytic subunit (residues F250-K887).
Membrane Composition
Retain the membrane composition as in simulations of the full complex, with DOPC (60%), DOPE (20%), DOPS (5%), and POPI (15%).
Simulation Runs
Perform 1 µs production runs for ten independent replicates of the simulation system.
Maintain system pressure at 1 Bar and temperature at 310 °К using the Parrinello-Rahman barostat and velocity-rescaling thermostat.
Electrostatic Interactions
Treat long-range electrostatic interactions using the smooth particle mesh Ewald method with charge interpolation through fourth-order B-splines.
Analysis
Monitor the time-resolved distance between the inositol 3’-O of POPI lipids and the gamma phosphate of ATP. For each frame, consider only the closest distance.